- s -

• sa_faraggi_max() : protocols::frag_picker
• safe_read() : core::chemical::gasteiger
• safe_secstruct() : protocols::jumping
• safe_set_conf() : protocols::environment
• safe_set_extended_torsions_and_idealize_loops() : protocols::loops
• safe_write() : core::chemical::gasteiger
• same_link() : core::io
• same_polarization_group() : core::scoring
• same_pose() : protocols::denovo_design
• sample_all_rotations_at_jump() : protocols::toolbox::sample_around
• sample_layer_lines_from_bins() : core::scoring::fiber_diffraction
• SASAShouldItCount() : core::scoring
• satisfies_restriction() : core::fragment::rna
• save_schema() : protocols::rosetta_scripts
• saved_native_pose() : core::pose
• saved_reference_pose() : core::pose , protocols::rosetta_scripts
• scalar_weighted() : protocols::constraint_generator
• SCORE12_PATCH() : core::scoring
• SCORE13() : core::scoring
• SCORE4_SMOOTH_CART() : core::scoring
• score_atom_centrally() : core::scoring::mm
• score_cst() : protocols::abinitio::abscript
• SCORE_FRAG_STORE() : protocols::loops::loop_closure::ccd
• score_function_subtag_complex_type_namer() : protocols::parser
• score_function_subtag_group() : protocols::parser
• score_function_tag_group() : protocols::parser
• score_mapping() : core::io::pose_from_sfr
• score_sort_criterion() : protocols::stepwise::modeler::rna
• score_type_filter_tracer() : protocols::score_filters
• score_type_for_orb_params() : core::scoring::orbitals
• score_type_from_name() : core::scoring
• scorefxn_is_symmetric() : core::pose::symmetry
• scorefxn_update_from_options() : protocols::enzdes::enzutil
• scores_to_alignments() : protocols::legacy_sewing
• sealed_symmetric_fold_tree() : core::pose::symmetry
• search_x() : core::scoring::packstat
• secant() : core::scoring::fiber_diffraction
• section() : protocols::sparta
• see_edge_or_core_or_loop_or_short_edge() : protocols::features::strand_assembly
• see_whether_model_is_H_bonded_by_terminal_strands() : protocols::legacy_sewing
• see_whether_sheet_is_antiparallel() : protocols::features::strand_assembly
• see_whether_sheets_can_be_combined() : protocols::features::strand_assembly
• see_whether_this_sw_has_SS_bond() : protocols::features::strand_assembly
• select_best_poses() : protocols::ligand_docking
• select_cav_balls() : core::scoring::packstat
• select_coord_for_residue() : core::select::util
• select_epitope_residues() : protocols::antibody
• select_interface_residues() : protocols::interface
• select_loop_frags() : protocols::loops
• select_loop_residues() : protocols::loops
• select_RBsegments() : protocols::rbsegment_relax
• selection_positions() : core::select::residue_selector
• separate_definitions_from_comments() : update_ResidueType_enum_files
• seq_design_strategy_to_enum() : protocols::antibody::design
• seq_design_strategy_to_string() : protocols::antibody::design
• seq_num_sort_criterion() : protocols::stepwise::modeler::rna
• seq_pdb_str() : protocols::dna
• seq_to_str() : protocols::dna
• seqpos_is_base_step_anchor() : core::scoring::dna
• seqs_from_cmd_lines() : core::sequence
• sequence_map_from_pdbinfo() : core::pose
• sequencealign() : protocols::frag_picker::scores
• serialize_graph_json() : protocols::legacy_sewing
• serialize_ids() : protocols::features
• serialize_residue_xyz_coords() : protocols::features
• serialized_loops_from_string() : protocols::loops
• set_asymm_unit_fold_tree() : core::conformation::symmetry , core::pose::symmetry
• set_base_partner() : core::scoring::dna
• set_base_segment_chainbreak_constraints() : protocols::dna
• set_bb_movemap() : protocols::hydrate
• set_bb_torsion() : core::pose
• set_bfactors_from_atom_id_map() : core::pose
• set_CCD_torsions_to_zero() : protocols::stepwise::modeler::rna
• set_chi_according_to_coordinates() : core::conformation
• set_constraints() : protocols::rbsegment_relax
• set_dew_waters_not_to_be_included() : protocols::hydrate
• set_difference() : protocols::denovo_design , protocols::stepwise::modeler::rna
• set_dihedrals() : protocols::denovo_design::components
• set_dihedrals_from_linkage_conformer_data() : core::pose::carbohydrates
• set_extended_torsions() : protocols::loops
• set_extended_torsions_and_idealize_loops() : protocols::loops
• set_externally_generated_packer_solution() : core::pack::interaction_graph
• set_fold_tree_from_symm_data() : core::conformation::symmetry
• set_full_model_info() : core::pose::full_model_info
• set_gaussian_stdevs() : protocols::recces::scratch
• set_gaussian_stdevs_recces_turner() : protocols::recces
• set_gaussian_stdevs_recces_turner_from_secstruct() : protocols::recces
• set_gaussian_stdevs_recces_turner_legacy() : protocols::recces
• set_gaussian_stdevs_thermal_sampler() : protocols::recces
• set_glycan_iupac_bb_torsions() : core::pose::carbohydrates
• set_glycan_iupac_chi_torsions() : core::pose::carbohydrates
• set_glycosidic_torsion() : core::conformation::carbohydrates , core::pose::carbohydrates
• set_jumps() : protocols::ligand_docking
• set_ligpose_rotamer() : protocols::match
• set_local_movemap() : protocols::vip
• set_loop_cutpoint_in_pose_fold_tree() : protocols::loops
• set_loop_pose() : protocols::generalized_kinematic_closure
• set_map_data() : protocols::denovo_design::components
• set_mmtf_default_options() : core::io::mmtf
• set_model_index_if_not_empty() : core::io::mmtf
• set_move_map_for_centroid_loop() : protocols::loops
• set_native_cdr_sequence() : protocols::antibody::design
• set_native_in_mover() : protocols::jd2
• set_nucleotide_to_A_form() : protocols::stepwise::legacy::modeler::rna
• set_output_res_and_chain() : core::pose
• set_pose_and_scorefxn_for_edens_scoring() : protocols::electron_density
• set_pose_secstruct() : core::select::residue_selector
• set_protocol_and_batch_id() : protocols::features
• set_r_array() : core::scoring::fiber_diffraction
• set_r_inv_array() : core::scoring::fiber_diffraction
• set_rb_constraints() : protocols::rbsegment_relax
• set_reasonable_fold_tree() : core::pose
• set_repulsive_bb_cores() : protocols::ligand_docking
• set_residue_pair_xform() : core::scoring::motif
• set_rna_secstruct_legacy() : core::pose::rna::secstruct_legacy
• set_rotamer_sampling_data_for_RLT() : core::pack::task::operation
• set_sampler_gaussian_stdev() : protocols::recces
• set_scorefxn_from_tag() : protocols::loop_modeling::utilities
• set_secstruct_from_dssp() : protocols::loops
• set_secstruct_from_psipred_ss2() : protocols::loops
• set_single_loop_fold_tree() : protocols::forge::methods , protocols::loops
• set_sphere() : protocols::ligand_docking
• set_ss_from_phipsi() : core::pose
• set_task_and_movemap() : protocols::hydrate
• set_task_factory_from_tag() : protocols::loop_modeling::utilities
• set_task_with_de_novo_water_using_resfile() : protocols::hydrate
• set_to_origin() : protocols::toolbox::rigid_body
• set_union() : protocols::stepwise::modeler::rna
• set_up_mapfile_reassignments_from_commandline() : core::chemical
• set_up_packer_palette() : core::pack::task
• set_up_params_for_move() : protocols::stepwise::monte_carlo::mover
• set_vdw_cached_rep_screen_info() : protocols::scoring
• set_vdw_cached_rep_screen_info_from_pose() : protocols::scoring
• set_water_info_and_add_de_novo_water() : protocols::hydrate
• set_water_numbers_to_zero() : protocols::magnesium
• set_xyz_coord() : protocols::fibril
• SetCrystWeightMover_subelement_ct_name() : protocols::cryst
• setPoseExtraScore() : core::pose
• setup_A_LH_foldtree() : protocols::antibody
• setup_aa2name() : core::chemical
• setup_aa2oneletter() : core::chemical
• setup_atom_id_map() : core::pose::copydofs
• setup_atom_id_map_match_atom_names() : core::pose::copydofs
• setup_atom_links() : core::conformation
• setup_atom_pair_constraints() : protocols::medal
• setup_atom_type_reassignments_from_commandline() : core::chemical
• setup_atomic_charge_reassignments_from_commandline() : core::chemical
• setup_base_pair_constraints() : core::pose::rna
• setup_bgres_cops() : core::pack
• setup_bulge_jump_point() : protocols::stepwise::legacy::modeler::rna
• setup_cdr_template() : protocols::tcr
• setup_cdr_template_from_db() : protocols::tcr
• setup_cdr_template_from_pdbid() : protocols::tcr
• setup_centroid_constraints() : protocols::hybridization
• setup_centroid_scatter() : core::scoring::fiber_diffraction
• setup_chain_break_jump_point() : protocols::stepwise::legacy::modeler::rna
• setup_chain_break_variants() : protocols::stepwise::modeler::rna
• setup_coarse_chainbreak_constraints() : protocols::rna::denovo
• setup_conformer_map() : protocols::motifs
• setup_constraints() : protocols::hybridization , protocols::medal , protocols::star
• setup_convergence_checks_from_cmdline() : protocols::canonical_sampling::mc_convergence_checks
• setup_coordinate_constraints() : protocols::medal
• setup_copy_DOF_input() : protocols::stepwise::legacy::modeler::rna
• setup_corresponding_atoms() : core::conformation
• setup_cylindrical_coords() : core::scoring::fiber_diffraction
• setup_disconnected() : protocols::rbsegment_relax
• setup_dme_point_graph() : protocols::simple_moves
• setup_dock_jump() : protocols::docking
• setup_dof_mask_from_move_map() : core::pose
• setup_dof_to_torsion_map() : core::pose
• setup_edges_for_partner() : protocols::docking
• setup_element2name() : core::chemical::element
• setup_existing_glycans() : core::pose::carbohydrates
• setup_faraggi_map() : protocols::frag_picker
• setup_filter_stats() : protocols::ncbb
• setup_fold_trees() : core::import_pose
• setup_foldtree() : protocols::docking
• setup_foldtree_from_anchors() : protocols::membrane
• setup_foldtree_pose_com() : protocols::membrane
• setup_for_density_scoring() : core::import_pose
• setup_for_dna() : protocols::relax
• setup_form_factors() : core::scoring::fiber_diffraction
• setup_fullatom_constraints() : protocols::hybridization
• setup_fw_template() : protocols::tcr
• setup_fw_template_from_db() : protocols::tcr
• setup_fw_template_from_pdbid() : protocols::tcr
• setup_geometric_attribute_list() : protocols::toolbox::match_enzdes_util
• setup_icoor_reassignments_from_commandline() : core::chemical
• setup_jumps() : core::import_pose
• setup_LH_A_foldtree() : protocols::antibody
• setup_links() : core::conformation
• setup_links_simple() : core::conformation
• setup_matching_atoms_with_given_names() : core::scoring
• setup_matching_CA_atoms() : core::scoring
• setup_matching_heavy_atoms() : core::scoring
• setup_matching_protein_backbone_heavy_atoms() : core::scoring
• setup_membrane_topology() : protocols::relax
• setup_name2aa() : core::chemical
• setup_name2element() : core::chemical::element
• setup_name2type() : protocols::frag_picker
• setup_oneletter2aa() : core::chemical
• setup_orientation_template() : protocols::tcr
• setup_packer() : protocols::mpi_refinement
• setup_packer_task() : protocols::antibody
• setup_patch_atomic_charge_reassignments_from_commandline() : core::chemical
• setup_pert_foldtree() : protocols::ncbb
• setup_pose_from_rbsegs() : protocols::rbsegment_relax
• setup_pose_input_stream() : protocols::stepwise::modeler::protein
• setup_pose_rbsegs_keep_loops() : protocols::rbsegment_relax
• setup_pose_setup_class() : protocols::stepwise::legacy::modeler::rna
• setup_pose_with_moving_residue_alternative_list() : protocols::stepwise::modeler::rna::rigid_body
• setup_protein_backbone_atom_id_map() : protocols::stepwise::modeler::protein
• setup_rmsd_atom_names() : core::scoring
• setup_rna_working_parameters() : protocols::stepwise::legacy::modeler::rna
• setup_sampler() : protocols::stepwise::sampler::rna
• setup_score() : protocols::abinitio::abscript , protocols::star
• setup_simple_fold_tree() : protocols::stepwise::legacy::modeler::rna
• setup_simple_full_length_rna_working_parameters() : protocols::stepwise::legacy::modeler::rna
• setup_single_loop_double_arm_remodeling_foldtree() : protocols::grafting
• setup_single_loop_single_arm_remodeling_foldtree() : protocols::grafting
• setup_star_topology() : protocols::rbsegment_relax
• setup_suite_atom_id_map() : protocols::stepwise::modeler::rna
• setup_symmetric_conformation() : core::conformation::symmetry
• setup_template_from_pdbfile() : protocols::tcr
• setup_three_prime_phosphate_based_on_next_residue() : core::pose::rna
• setup_type2name() : protocols::frag_picker
• setup_unified_stepwise_modeler() : protocols::stepwise::monte_carlo::mover
• setup_user_coordinate_constraints() : protocols::hybridization
• setup_user_defined_jumps() : core::import_pose
• setup_vall_cheating_fragments() : protocols::frags
• setup_vall_fragments() : protocols::frags
• setup_vary_polar_hydrogen_geometry() : protocols::simple_moves
• setup_vary_rna_bond_geometry() : protocols::simple_moves
• setup_water_bank_for_magnesiums() : core::import_pose
• setup_water_builders_for_residue_type() : core::scoring::lkball
• setup_working_parameters_explicit() : protocols::stepwise::modeler::working_parameters
• setup_working_parameters_for_swa() : protocols::stepwise::modeler::working_parameters
• sfr_to_sd() : core::io::mmtf
• sfrs_to_sd() : core::io::mmtf
• sgn() : core::io::pose_from_sfr
• share_axis_atoms() : core::scoring::power_diagram
• shift_jump_numbers_in_dofs() : core::conformation::symmetry
• shift_jumps() : protocols::forge::methods
• short_ss_loop_filter() : protocols::evolution::AlignmentCleanerTools
• shortest_path() : core::chemical
• ShortToRealAngle() : protocols::loophash
• ShouldItCount() : core::scoring
• show_accuracy_report() : protocols::rna::movers
• show_atom_tree() : core::conformation
• show_base_pair_params() : core::scoring::dna
• show_base_pair_params_with_z_scores() : core::scoring::dna
• show_base_step_params() : core::scoring::dna
• show_detail() : core::scoring
• show_dna_geometry() : core::scoring::dna
• show_foldtree() : core::conformation::symmetry
• show_new_base_step_params() : core::scoring::dna
• show_residue_connections() : core::io::pose_from_sfr
• show_scorefxn_weight_lines() : protocols::stepwise::modeler::rna
• show_water_hb_network() : protocols::hydrate
• sidechain_rmsd_filter_tracer() : protocols::simple_filters
• sigmoid() : protocols::noesy_assign
• sigmoidish_neighbor() : core::scoring::packing
• sigmoidish_neighbor_deriv() : core::scoring::packing
• SilentEnergy_sort_by_name() : core::io::silent
• simple_fold_tree() : protocols::antibody , protocols::antibody_legacy , protocols::star
• simple_mapping_from_file() : core::sequence
• simple_numeric_deriv_check() : core::optimization
• simple_one_loop_fold_tree() : protocols::antibody , protocols::antibody_legacy
• simple_visualize_fold_tree() : core::kinematics
• simple_visualize_fold_tree_and_movemap() : core::kinematics
• simple_visualize_fold_tree_and_movemap_bb_chi() : core::kinematics
• simplifyWhiteSpace() : protocols::sparta
• single_ligand_motif_from_stream() : protocols::motifs
• single_motif_from_filename() : protocols::motifs
• single_motif_from_stream() : protocols::motifs
• single_residue_from_stream() : protocols::motifs
• skip_redundant_constraints() : core::scoring::constraints
• sleep() : protocols::stepwise::modeler::rna
• slice() : protocols::stepwise::modeler
• slice_out_pose() : protocols::stepwise::modeler
• slide_into_contact_and_score() : protocols::sic_dock
• slide_into_contact_and_score_DEPRICATED() : protocols::sic_dock
• slide_jump() : protocols::denovo_design
• slide_together_tracer() : protocols::ligand_docking
• smallmer_from_largemer() : protocols::forge::methods
• SOFT_REP_DESIGN_WTS() : core::scoring
• SOFT_REP_WTS() : core::scoring
• sort_by_binding() : protocols::ligand_docking
• sort_by_length() : protocols::fldsgn::topology
• sort_by_second() : protocols::ligand_docking
• sort_copy_dofs() : protocols::stepwise::modeler::rna
• sort_function() : protocols::frag_picker
• sort_jobsummaries_list() : protocols::cyclic_peptide_predict
• sort_new_rotamers_into_rotset_vector() : core::pack::rotamer_set
• sort_numerically_ascending() : protocols::ddg
• sort_pair_list() : protocols::stepwise::legacy::modeler::rna
• sort_patchop_by_name() : core::chemical
• sort_pose_by_score() : core::pose
• sort_PoseWithScore() : protocols::abinitio
• sort_residue_type_pointers_by_name() : protocols::toolbox::match_enzdes_util
• sort_scores() : protocols::frag_picker::scores
• sort_seq_num_list() : protocols::stepwise::modeler::rna
• sort_xbond_func() : core::io::mmtf
• spanfile_name() : core::conformation::membrane
• spanfile_names() : core::conformation::membrane
• spearman() : protocols::ligand_docking
• spherical() : protocols::fldsgn::potentials::sspot
• SpliceIn_complex_type_name_for_subsubtag() : protocols::splice
• SpliceIn_complex_type_name_for_subtag() : protocols::splice
• SpliceInAntibody_complex_type_name_for_subsubtag() : protocols::splice
• SpliceInAntibody_complex_type_name_for_subtag() : protocols::splice
• SpliceInTail_complex_type_name_for_subsubtag() : protocols::splice
• SpliceInTail_complex_type_name_for_subtag() : protocols::splice
• SpliceOut_complex_type_name_for_subsubtag() : protocols::splice
• SpliceOut_complex_type_name_for_subtag() : protocols::splice
• SpliceOutAntibody_complex_type_name_for_subsubtag() : protocols::splice
• SpliceOutAntibody_complex_type_name_for_subtag() : protocols::splice
• SpliceOutTail_complex_type_name_for_subsubtag() : protocols::splice
• SpliceOutTail_complex_type_name_for_subtag() : protocols::splice
• spline_coeffs() : core::scoring::electron_density
• split() : protocols::sparta
• split_by_ca_ca_dist() : protocols::loops
• split_by_resSeq() : protocols::loops
• split_mid_ranges() : protocols::fold_from_loops::utils
• split_pose() : protocols::stepwise::modeler
• split_segments_longer_than_6mers() : core::fragment::rna
• split_sequence_motif() : core::sequence
• split_string_based_on_inserts() : protocols::pdbinfo_manipulations
• split_topology_by_chain_noshift() : protocols::membrane
• split_topology_by_jump() : protocols::membrane
• split_topology_by_jump_noshift() : protocols::membrane
• SPLIT_UNFOLDED_BOLTZ() : core::scoring
• SPLIT_UNFOLDED_ELE() : core::scoring
• SPLIT_UNFOLDED_MEAN() : core::scoring
• SPLIT_UNFOLDED_MEDIAN() : core::scoring
• SPLIT_UNFOLDED_MM() : core::scoring
• SPLIT_UNFOLDED_MODE() : core::scoring
• SPLIT_UNFOLDED_PDB() : core::scoring
• SPLIT_UNFOLDED_ROSETTA() : core::scoring
• SPLIT_UNFOLDED_UNIQUE() : core::scoring
• SPLIT_UNFOLDED_USER_DEFINED() : core::scoring
• split_up_remark_line() : protocols::toolbox::match_enzdes_util
• split_WhiteSpace() : protocols::sparta
• SQ() : core::scoring::electron_density
• sqr() : core::scoring::membrane , core::scoring::methods , core::scoring::motif , core::scoring::packing , core::scoring , protocols::cartesian , protocols::kinmatch , protocols::loophash , protocols::sic_dock
• square() : core::scoring::electron_density , core::scoring::electron_density_atomwise , core::scoring::fiber_diffraction , protocols::rbsegment_relax
• Srfp_complex_type_name_for_subsubtag() : protocols::splice
• Srfp_complex_type_name_for_subtag() : protocols::splice
• ss_index() : protocols::frag_picker::quota
• ss_length_check() : protocols::frags
• star_fold_tree() : protocols::protein_interface_design
• StarAbinitio_main() : protocols::star
• START_BLOCK() : protocols::jd2
• steal_alignment() : core::sequence
• steal_constant_length_frag_set_from_pose() : core::fragment
• steal_frag_set_from_pose() : core::fragment
• steal_ligands() : protocols::comparative_modeling
• stepwise_addable_pose_residue() : core::pose
• stepwise_addable_residue() : core::pose
• store_base_residue_type_name_in_sfr() : core::io::pdb
• store_chain_sequence_record_in_sfr() : core::io::pdb
• store_cis_peptide_record_in_sfr() : core::io::pdb
• store_connection_architect() : protocols::denovo_design::connection
• store_crystallographic_parameter_record_in_sfr() : core::io::pdb
• store_CSA_in_pose() : core::scoring
• store_DC_in_pose() : core::scoring
• store_denovo_architect() : protocols::denovo_design::architects
• store_distance_snapshot() : protocols::noesy_assign
• store_distmap_with_namedatoms() : protocols::noesy_assign
• store_formula_record_in_sfr() : core::io::pdb
• store_heterogen_name_record_in_sfr() : core::io::pdb
• store_heterogen_synonym_record_in_sfr() : core::io::pdb
• store_link_record_in_sfr() : core::io::pdb
• store_mod_res_record_in_sfr() : core::io::pdb
• store_RDC_in_pose() : core::scoring
• store_RDC_ROHL_in_pose() : core::scoring
• store_RDC_segments_in_pose() : protocols::scoring
• store_ssbond_record_in_sfr() : core::io::pdb
• store_unknown_records_in_sfr() : core::io::pdb
• str() : protocols::kinmatch
• strand_orientation_vector() : core::scoring::dna
• streams_from_cmd_line() : core::import_pose::pose_stream
• string_from_type_set_mode() : core::chemical
• string_has_suffix() : protocols::relax
• string_join() : protocols::dna
• STRING_LIST() : core::chemical
• string_to_experimental_technique() : core::io::rcsb
• string_to_hb_eval_type() : core::scoring::hbonds
• string_to_icoord_type() : core::chemical
• string_to_int() : core::pose::rna , core::scoring::rna::chemical_shift , protocols::stepwise::modeler::rna
• string_to_real() : core::scoring::rna::chemical_shift , protocols::stepwise::modeler::rna
• string_to_size_vector() : protocols::rna::movers
• strip_brackets() : core::io::nmr
• strip_out_magnesiums() : protocols::magnesium
• strip_spacers() : core::sequence
• strip_whitespace() : core::chemical::orbitals , core::scoring::packing
• struct_ids_from_tag() : protocols::features
• stub_from_points() : protocols::hotspot_hashing
• stub_id_to_named_stub_id() : core::conformation , core::pose
• stub_tgt_angle() : protocols::hotspot_hashing
• stub_to_points() : protocols::hotspot_hashing
• sub_to_full() : core::pose::full_model_info
• substitute_residue() : protocols::dna
• subtag_for_backrubdd() : protocols::protein_interface_design::movers
• subtag_for_bbgrid() : protocols::helical_bundle
• subtag_for_bundgrid() : protocols::helical_bundle
• subtag_for_cyclize() : protocols::cyclic_peptide
• subtag_for_hotspothasher() : protocols::protein_interface_design::movers
• subtag_for_match_type() : protocols::fldsgn
• subtag_for_msd() : protocols::protein_interface_design::movers
• subtag_for_multiple_sigmoids() : protocols::calc_taskop_filters
• subtag_for_SetupHotspotConstraintsLoopsMover() : protocols::protein_interface_design::movers
• subtag_for_SetupHotspotConstraintsMover() : protocols::protein_interface_design::movers
• subtract() : protocols::mean_field
• subtract_chi_angles() : core::pack::dunbrack
• sugar_modifications_from_suffix() : core::io::carbohydrates
• suite_rmsd() : protocols::stepwise::modeler::rna
• suite_square_deviation() : protocols::stepwise::modeler::rna
• sum_constraint_scoreterms() : protocols::enzdes::enzutil
• sum_IntraNOE() : protocols::noesy_assign
• sum_peak_volumes() : protocols::noesy_assign
• sum_total_residue_energy() : protocols::protein_interface_design
• summary_string_to_type() : core::simple_metrics::metrics
• superimpose() : protocols::toolbox
• superimpose_all() : protocols::mpi_refinement
• superimpose_overhangs_heavy() : protocols::grafting
• superimpose_pose() : core::scoring
• superimpose_pose_legacy() : protocols::stepwise::modeler::align
• superimpose_pose_on_subset_bb() : protocols::fibril
• superimpose_pose_on_subset_CA() : protocols::toolbox::pose_manipulation
• superimpose_with_stepwise_aligner() : protocols::stepwise::modeler::align
• superposition_transform() : protocols::seeded_abinitio , protocols::toolbox
• surrogate_atom_for_orbital() : core::scoring::orbitals
• swap() : core::id
• swap4_aligned() : core::scoring::electron_density , core::scoring::electron_density_atomwise
• swap_bytes() : core::io::serialization
• swap_seqpos() : core::scoring::methods
• swap_transform() : core::pose
• switch_focus_among_poses_randomly() : protocols::stepwise::modeler
• switch_focus_to_other_pose() : protocols::stepwise::modeler
• switch_to_centroid_rot_set() : core::util
• switch_to_residue_type_set() : core::util
• sym_dof_jump_num() : core::pose::symmetry
• sym_dof_names() : core::pose::symmetry
• sym_rmsd_with_super_subset() : core::scoring
• SymDock_main() : protocols::symmetric_docking
• symmetric_components() : core::pose::symmetry
• symmetric_fold_tree() : protocols::denovo_design
• symmetric_repackable_residues() : core::pack
• symmetric_residue_subset() : protocols::denovo_design
• symmetric_rotamer_trials() : core::pack
• symmetric_secstruct() : protocols::denovo_design
• symmetrize_fold_tree() : core::conformation::symmetry , core::pose::symmetry
• symmetrize_spans() : protocols::membrane::symmetry
• symmetrizeBfactors() : protocols::electron_density
• symmetry_info() : core::pose::symmetry
• SymMinimizeInterface() : protocols::protein_interface_design